SnowShoes-FTD – Find Fusions from RNA-Seq data

SnowShoes-FTD

:: DESCRIPTION

SnowShoes-FTD is a bioinformatics tool to identify fusion transcripts from paired-end transcriptome sequencing data. The tool employs multiple steps of false positive filtering and nominates the fusion candidates with high confidence (approaching 100% true positive rate). The unique features of SnowShoes-FTD include: (i) the ability to discover multiple fusion isoforms in which the two gene partners give rise to transcripts with different junctions; (ii) prediction of potential fusion mechanisms including inversion, translocation, and/or interstitial deletions; (iii) identification of whether the junction point in a fusion transcript occurs at the boundaries of known exons which implies the fusion events might have happened inside an intron in DNA and transcribed to the fusion transcript.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Please contact the author, Yan W. Asmann, Ph.D. smann.yan@mayo.edu

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Aug;39(15):e100. Epub 2011 May 27.
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.

Barnacle 1.0.4 – Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assembly

Barnacle 1.0.4

:: DESCRIPTION

Barnacle (Browsing Assembled RNA for Chimeras with Localized Evidence) is a pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Barnacle

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.
Swanson L et al.

FACTERA 1.3 – Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm

FACTERA 1.3

:: DESCRIPTION

FACTERA is a tool for practical and robust de novo enumeration of genomic fusions and breakpoints from paired-end targeted (or genome-wide) sequencing data.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FACTERA

:: MORE INFORMATION

Citation

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution.
Newman AM, Bratman SV, Stehr H, Lee LJ, Liu CL, Diehn M, Alizadeh AA.
Bioinformatics. 2014 Aug 20. pii: btu549.

ViralFusionSeq 20160817 – Discover Viral Integration Events and Fusion Transcripts

ViralFusionSeq 20160817

:: DESCRIPTION

ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution.

::DEVELOPER

ViralFusionSeq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Perl

:: DOWNLOAD

 ViralFusionSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 1;29(5):649-51. doi: 10.1093/bioinformatics/btt011. Epub 2013 Jan 12.
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF.

Pegasus 0.3.1 – Fusion Annotation and Prediction

Pegasus 0.3.1

:: DESCRIPTION

Pegasus annotates biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, annotation of reading frame events, reconstruction of novel fusion proteins, annotation of preserved functional domains (e.g. kinases).

::DEVELOPER

EDA (Electronic Design Automation Group)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

  Pegasus

:: MORE INFORMATION

Citation

Abate F., Zairis S., Ficarra E., Acquaviva A., Wiggins C.H., Frattini V., Lasorella A., Iavarone A., Inghirami G., Rabadan R.,
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
BMC SYSTEMS BIOLOGY vol. 8 n. 97, 2014. DOI: 10.1186/s12918-014-0097-z

FUSION – de novo Protein Structure Prediction

FUSION

:: DESCRIPTION

FUSION is a fragment-free probabilistic graphical model for conformational sampling in continuous space and assess its accuracy using ‘blind’ protein targets with a length up to 250 residues from the CASP11 structure prediction exercise.

::DEVELOPER

FUSION team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Improving Protein Fold Recognition by Deep Learning Networks.
Jo T, Hou J, Eickholt J, Cheng J.
Sci Rep. 2015 Dec 4;5:17573. doi: 10.1038/srep17573.

Exit mobile version